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Kang, R.

Publications and source records attributed to Kang, R..

7 recordsLinked to original sources

Single Cell RNA-Seq Analysis of Regenerative Drug-Treated Human Pancreatic Islets Identifies A Cycling Alpha Cell Population As Key Beta Cell Progenitors

Diabetes ultimately results from an inadequate number of functional, insulin-producing human beta cells. Although current attempts to replenish the remaining beta cell pool in people with diabetes are encouraging, scalability and cost limit access for the millions of people with diabetes. The small molecule DYRK1A inhibitor class of beta cell regenerative drugs, either alone or in combination with GLP1 receptor agonists or TGF{beta} superfamily inhibitors, are capable of inducing beta cell replication in vitro and increasing beta cell mass in vivo. Despite these advances, the precise mechanisms of action of DYRK1A inhibitors remain incompletely understood. To address the mechanisms more deeply, we performed single cell RNA sequencing on human pancreatic islets treated with a DYRK1A inhibitor, either alone, or in combination with a GLP1 receptor agonist or a TGF{beta} superfamily inhibitor. We identify a cluster of Cycling Alpha Cells as the cells most responsive to DYRK1A inhibition. Velocity and pseudotime lineage trajectory analyses suggest that Cycling Alpha Cells serve as the primary target cell type for of DYRK1A inhibitors, and may serve as precursor cells that transdifferentiate into functional human beta cells in response to the DYRK1A inhibition. In addition to providing a novel mechanism of action for DYRK1A inhibitors, our findings suggest that efforts to target regenerative drugs to human beta cells may be mis-directed: the proper target may be Cycling Alpha Cells.

cell biology↗

Sequence-based prediction of the solubility of peptides containing non-natural amino acids

Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs, as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the solubility of mAA-containing peptides. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different mAAs for a total number of 30 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm.

biophysics↗

High-quality nuclear genome and mitogenome of Bipolaris sorokiniana strain LK93, a devastating pathogen causing wheat root rot

Bipolaris sorokiniana, one of the most devastating hemibiotrophic fungal pathogens, causes root rot, crown rot, leaf blotching, and black embryos of gramineous crops worldwide, posing a serious threat to global food security. However, the host-pathogen interaction mechanism between B. sorokiniana and wheat remains poorly understood. To facilitate related studies, we sequenced and assembled the genome of B. sorokiniana strain LK93. Nanopore long reads and next generation sequencing short reads were applied in the genome assembly, and the final 36.4 Mb genome assembly contains 16 contigs with the contig N50 of 2.3 Mb. Subsequently, we annotated 11,811 protein-coding genes including 10,620 functional genes, 258 of which were identified as secretory proteins including 211 predicted effectors. Additionally, the 111,581 bp mitogenome of LK93 was assembled and annotated. The LK93 genomes presented in this study will facilitate research in the B. sorokiniana-wheat pathosystem for better control of crop diseases.

plant biology↗

Genetic dissection of crossover mutants defines discrete intermediates in mouse meiosis

Crossovers, the exchange of homolog arms, are required for accurate segregation during meiosis. Studies in yeast have established that the single end invasion intermediate is highly regulated to ensure crossover distribution. Single end invasions are thought to differentiate into double Holliday junctions that are resolved by MutLgamma (MLH1/3) into crossovers. Currently, we lack knowledge of early steps of mammalian crossover recombination or how intermediates are differentiated in any organism. Using comprehensive analysis of recombination and cytology, we infer that polymerized single-end invasion intermediates and nicked double Holliday junctions are crossover precursors in mouse spermatocytes. In marked contrast to yeast, MLH3 plays a structural role to differentiate single end invasions into double Holliday junctions with differentially polymerized 3 ends. Therefore, we show independent genetic requirements for precursor formation and asymmetry with regard to 3 end processing, providing mechanistic insight into crossover formation and patterning.

genetics↗

Sequence-based pH-dependent prediction of protein solubility using CamSol

Solubility is a property of central importance for the use of proteins in research and in applications in biotechnology and medicine. Since experimental methods for measuring protein solubility are resource-intensive and time-consuming, computational methods have recently emerged to enable the rapid and inexpensive screening of large libraries of proteins, as it is routinely required in development pipelines. Here, we describe the extension of one of such methods, CamSol, to include in the predictions the effect of the pH of the solubility. We illustrate the accuracy of the pH-dependent predictions on a variety of antibodies and other proteins.

biophysics↗

Extracellular matrix guidance determines proteolytic and non-proteolytic cancer cell patterning

Metastatic tumor cell invasion into interstitial tissue is a mechanochemical process that responds to tissue cues and further involves proteolytic remodeling of the tumor stroma. How matrix density, tissue guidance and the ability of proteolytic tissue remodeling cooperate and determine decision-making of invading tumor cells in complex-structured three-dimensional (3D) tissue remains unclear. We here developed a collagen-based invasion assay containing a guiding interface of low collagen density adjacent to randomly organized 3D fibrillar lattice and examined the invasion of melanoma cells from multicellular spheroids in response to matrix density, guidance cues and collagenolysis. After 48 hours of culture, two invasion niches developed, (i) sheet-like collective migration along the interface and (ii) single cell- and strand-like invasion into randomly organized 3D matrix. High collagen density impeded migration into the random matrix, whereas migration along a high-density collagen interface was increased compared to the low-density matrix assay. In silico analysis predicted that facilitated interface migration in high-density matrix depended on physical guidance without collagen degradation, whereas migration into randomly organized matrix was strongly dependent on collagenolysis. When tested in 3D culture, inhibition of matrix metalloprotease (MMP)-mediated collagen degradation compromised migration into random matrix in dependence of density, whereas interface-guided migration remained effective. In conclusion, with increasing tissue density, matrix cues bordered by dense matrix, but not randomly organized matrix, support effective MMP-independent migration. This identifies the topology of interstitial tissue a primary determinant of switch behaviors between MMP-dependent and MMP-independent cancer cell invasion.

cancer biology↗

The timescale and magnitude of aperiodic activity decreases with cortical depth in humans, macaques and mice

Cortical dynamics obey a 1/f power law, exhibiting an exponential decay of spectral power with increasing frequency. The slope and offset of this 1/f decay reflect the timescale and magnitude of aperiodic neural activity, respectively. These properties are tightly linked to cellular and circuit mechanisms (e.g. excitation:inhibition balance and firing rates) as well as cognitive processes (e.g. perception, memory, and state). However, the physiology underlying the 1/f power law in cortical dynamics is not well understood. Here, we compared laminar recordings from human, macaque and mouse cortex to evaluate how 1/f aperiodic dynamics vary across cortical layers and species. We report that 1/f slope is steepest in superficial layers and flattest in deep layers in each species. Additionally, the magnitude of this 1/f decay is greatest in superficial cortex and decreases with depth. We could account for both of these findings with a simple model in which superficial cortical transmembrane currents had longer time constants and greater densities than those in deeper layers. Together, our results provide novel insight into the organization of cortical dynamics, suggesting that the amplitude and time constant of local currents control circuit processing as a function of laminar depth. This may represent a general mechanism to facilitate appropriate integration of fast sensory inputs (infragranular) with slow feedback-type inputs (supragranular) across cortical areas and species.

neuroscience↗